Related papers: Automated family-based naming of small RNAs for ne…
The automatic generation of computer programs is one of the main applications with practical relevance in the field of evolutionary computation. With program synthesis techniques not only software developers could be supported in their…
Machine learning (ML) is revolutionising drug discovery by expediting the prediction of small molecule properties essential for developing new drugs. These properties -- including absorption, distribution, metabolism and excretion (ADME)--…
Genomic data I used in many fields but, it has become known that most of the platforms used in the sequencing process produce significant errors. This means that the analysis and inferences generated from these data may have some errors…
To uncover the genetic basis of complex disease, individuals are often measured at a large number of genetic variants (usually SNPs) across the genome. GemTools provides computationally efficient tools for modeling genetic ancestry based on…
In microarray experiments, it is often of interest to identify genes which have a pre-specified gene expression profile with respect to time. Methods available in the literature are, however, typically not stringent enough in identifying…
Motivation: Laboratory gene regulatory data for a species are sporadic. Despite the abundance of gene regulatory network algorithms that employ single data sets, few algorithms can combine the vast but disperse sources of data and extract…
The problem of multilabel classification when the labels are related through a hierarchical categorization scheme occurs in many application domains such as computational biology. For example, this problem arises naturally when trying to…
Proper naming of methods can make program code easier to understand, and thus enhance software maintainability. Yet, developers may use inconsistent names due to poor communication or a lack of familiarity with conventions within the…
We have micromachined a silicon-chip device that transports DNA with a Brownian ratchet that rectifies the Brownian motion of microscopic particles. Transport properties for a DNA 50mer agree with theoretical predictions, and the DNA…
Repetitive DNA (repeats) poses significant challenges for accurate and efficient genome assembly and sequence alignment. This is particularly true for metagenomic data, where genome dynamics such as horizontal gene transfer, gene…
Multi-label classification is an important yet challenging task in natural language processing. It is more complex than single-label classification in that the labels tend to be correlated. Existing methods tend to ignore the correlations…
Microarray is a technology to quantitatively monitor the expression of large number of genes in parallel. It has become one of the main tools for global gene expression analysis in molecular biology research in recent years. The large…
Consider a general machine learning setting where the output is a set of labels or sequences. This output set is unordered and its size varies with the input. Whereas multi-label classification methods seem a natural first resort, they are…
Software Testing is a process to identify the quality and reliability of software, which can be achieved through the help of proper test data. However, doing this manually is a difficult task due to the presence of number of predicate nodes…
This paper presents EasyRAG, a simple, lightweight, and efficient retrieval-augmented generation framework for automated network operations. Our framework has three advantages. The first is accurate question answering. We designed a…
Deep learning, a rebranding of deep neural network research works, has achieved a remarkable success in recent years. With multiple hidden layers, deep learning models aim at computing the hierarchical feature representations of the…
We propose a dynamic neighborhood aggregation (DNA) procedure guided by (multi-head) attention for representation learning on graphs. In contrast to current graph neural networks which follow a simple neighborhood aggregation scheme, our…
Searching for similar genomic sequences is an essential and fundamental step in biomedical research and an overwhelming majority of genomic analyses. State-of-the-art computational methods performing such comparisons fail to cope with the…
LAGE is a systematic framework developed in Java. The motivation of LAGE is to provide a scalable and parallel solution to reconstruct Gene Regulatory Networks (GRNs) from continuous gene expression data for very large amount of genes. The…
Since microRNAs (miRNAs) play a crucial role in post-transcriptional gene regulation, miRNA identification is one of the most essential problems in computational biology. miRNAs are usually short in length ranging between 20 and 23 base…